Listening on http://127.0.0.1:44435 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 /scratch/cpanse/ Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:04065072:rsa routines:rsa_ossl_private_decrypt:padding check failed') Passing through unaltered. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:04065072:rsa routines:rsa_ossl_private_decrypt:padding check failed') Passing through unaltered. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_003_S560331_Liver_1_6umZirkoniumbeads_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_014_S560332_Liver_5mM_stealBeads_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_002_S560330_Liver_glassbeads_Group_1.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 409169 output$tic.basepeak <- renderPlot({ #rows are 409169 output$download 2... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. output$tic.basepeak <- renderPlot({ #rows are 409169 output$download 2... ggsave to file /tmp/Rtmp7sFAxI/rawDiag-384bcb1dca0ac.pdf generated pdf /tmp/Rtmp7sFAxI/rawDiag-384bcb1dca0ac.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293417, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 08:55:48", createdby = "spfammatter", deletable = "true", description = "input files:\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_002_S560330_Liver_glassbeads_Group_1.raw \np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_003_S560331_Liver_1_6umZirkoniumbeads_Group_2.raw\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_014_S560332_Liver_5mM_stealBeads_Group_3.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2356667)), modified = "2023-09-12 08:55:48", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2356693, container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 08:55:50", createdby = "spfammatter", deletable = "true", filechecksum = "de9ed376012b38b7c6d7ae019b3c4548", junk = "false", modified = "2023-09-12 08:55:50", modifiedby = "spfammatter", name = "WU293417-20230912-0855-rawDiag.pdf", relativepath = "container_32829/workunit_293417/WU293417-20230912-0855-rawDiag.pdf", size = "152012", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32829/workunit_293417/WU293417-20230912-0855-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32829/workunit_293417/WU293417-20230912-0855-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293417))) The current plot is available as workunit 293417 #rows are 409169 output$download 1... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_012_S560337_Pancrease_1_6umZirkoniumbeads_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_008_S560336_Pancrease_glassbeads_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_004_S560338_Pancrease_5mM_stealBeads_Group_3.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values output$tic.basepeak <- renderPlot({ #rows are 387452 output$download 2... ggsave to file /tmp/Rtmp7sFAxI/rawDiag-384bcb55bd6526.pdf generated pdf /tmp/Rtmp7sFAxI/rawDiag-384bcb55bd6526.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293418, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 08:56:56", createdby = "spfammatter", deletable = "true", description = "input files:\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_008_S560336_Pancrease_glassbeads_Group_1.raw \np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_012_S560337_Pancrease_1_6umZirkoniumbeads_Group_2.raw\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_004_S560338_Pancrease_5mM_stealBeads_Group_3.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2356677), list(`_classname` = "resource", `_id` = 2356675)), modified = "2023-09-12 08:56:56", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2356694, container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 08:56:58", createdby = "spfammatter", deletable = "true", filechecksum = "19e8cc4b122834a76a54f3a70c91f0dd", junk = "false", modified = "2023-09-12 08:56:58", modifiedby = "spfammatter", name = "WU293418-20230912-0856-rawDiag.pdf", relativepath = "container_32829/workunit_293418/WU293418-20230912-0856-rawDiag.pdf", size = "149368", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32829/workunit_293418/WU293418-20230912-0856-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32829/workunit_293418/WU293418-20230912-0856-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293418))) The current plot is available as workunit 293418 #rows are 387452 output$download 1... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_010_S560341_Ileume_5mM_stealBeads_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_015_S560340_Illeume_1_6umZirkoniumbeads_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_016_S560339_Ileume_glassbeads_Group_1.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values output$tic.basepeak <- renderPlot({ #rows are 395233 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 395233 output$download 2... ggsave to file /tmp/Rtmp7sFAxI/rawDiag-384bcb575f61e7.pdf generated pdf /tmp/Rtmp7sFAxI/rawDiag-384bcb575f61e7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293419, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 08:58:17", createdby = "spfammatter", deletable = "true", description = "input files:\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_016_S560339_Ileume_glassbeads_Group_1.raw \np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_015_S560340_Illeume_1_6umZirkoniumbeads_Group_2.raw\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_010_S560341_Ileume_5mM_stealBeads_Group_3.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2356676), list(`_classname` = "resource", `_id` = 2356671)), modified = "2023-09-12 08:58:17", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2356699, container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 08:58:18", createdby = "spfammatter", deletable = "true", filechecksum = "af237ce663d8801ac296b71794041b1d", junk = "false", modified = "2023-09-12 08:58:18", modifiedby = "spfammatter", name = "WU293419-20230912-0858-rawDiag.pdf", relativepath = "container_32829/workunit_293419/WU293419-20230912-0858-rawDiag.pdf", size = "161347", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32829/workunit_293419/WU293419-20230912-0858-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32829/workunit_293419/WU293419-20230912-0858-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293419))) The current plot is available as workunit 293419 #rows are 395233 output$download 1... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_007_S560334_Muscle_1_6umZirkoniumbeads_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_011_S560333_Muscle_glassbeads_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_006_S560335_Muscle_5mM_stealBeads_Group_3.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values output$tic.basepeak <- renderPlot({ #rows are 386362 output$download 2... ggsave to file /tmp/Rtmp7sFAxI/rawDiag-384bcb2900597e.pdf generated pdf /tmp/Rtmp7sFAxI/rawDiag-384bcb2900597e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293420, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 09:00:12", createdby = "spfammatter", deletable = "true", description = "input files:\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_011_S560333_Muscle_glassbeads_Group_1.raw \np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_007_S560334_Muscle_1_6umZirkoniumbeads_Group_2.raw\np32829/Proteomics/LUMOS_2/analytic_20230908/20230908_C32829_006_S560335_Muscle_5mM_stealBeads_Group_3.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2356674)), modified = "2023-09-12 09:00:12", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2356700, container = list(`_classname` = "order", `_id` = 32829), created = "2023-09-12 09:00:13", createdby = "spfammatter", deletable = "true", filechecksum = "998062aa2929450002ca0bcc61f2a207", junk = "false", modified = "2023-09-12 09:00:13", modifiedby = "spfammatter", name = "WU293420-20230912-0900-rawDiag.pdf", relativepath = "container_32829/workunit_293420/WU293420-20230912-0900-rawDiag.pdf", size = "249504", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32829/workunit_293420/WU293420-20230912-0900-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32829/workunit_293420/WU293420-20230912-0900-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293420))) The current plot is available as workunit 293420 #rows are 386362 output$download 1... Execution halted